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PDBsum entry 1dhy

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protein metals links
Oxidoreductase (oxygenase) PDB id
1dhy
Jmol
Contents
Protein chain
278 a.a. *
Metals
_FE
Waters ×39
* Residue conservation analysis
PDB id:
1dhy
Name: Oxidoreductase (oxygenase)
Title: Kks102 bphc enzyme
Structure: 2,3-dihydroxybiphenyl 1,2-dioxygenase. Chain: a. Synonym: kks102 bphc enzyme. Engineered: yes
Source: Pseudomonas sp.. Organism_taxid: 306. Gene: bphc. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.30Å     R-factor:   0.186     R-free:   0.246
Authors: T.Senda,K.Sugiyama,H.Narita,Y.Mitsui
Key ref:
T.Senda et al. (1996). Three-dimensional structures of free form and two substrate complexes of an extradiol ring-cleavage type dioxygenase, the BphC enzyme from Pseudomonas sp. strain KKS102. J Mol Biol, 255, 735-752. PubMed id: 8636975 DOI: 10.1006/jmbi.1996.0060
Date:
07-Jul-95     Release date:   15-Oct-95    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P17297  (BPHC_PSES1) -  Biphenyl-2,3-diol 1,2-dioxygenase
Seq:
Struc:
293 a.a.
278 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.13.11.39  - Biphenyl-2,3-diol 1,2-dioxygenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Biphenyl-2,3-diol + O2 = 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate
Biphenyl-2,3-diol
+ O(2)
= 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate
      Cofactor: Mn(2+) or Fe cation
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   4 terms 
  Biochemical function     catalytic activity     7 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.1996.0060 J Mol Biol 255:735-752 (1996)
PubMed id: 8636975  
 
 
Three-dimensional structures of free form and two substrate complexes of an extradiol ring-cleavage type dioxygenase, the BphC enzyme from Pseudomonas sp. strain KKS102.
T.Senda, K.Sugiyama, H.Narita, T.Yamamoto, K.Kimbara, M.Fukuda, M.Sato, K.Yano, Y.Mitsui.
 
  ABSTRACT  
 
The crystal structure of an enzyme having polychlorinated-biphenyl degrading activity, the BphC enzyme from Pseudomonas sp. strain KKS102, has been solved as a free form at 1.8 A resolution. This is the first three-dimensional structure among the extradiol-type dioxygenases. Based on 34,387 reflections (10.0 to 1.8 A, completeness 87.8%), a current R-factor of 20.4% (with a free R-factor of 24.3%) was obtained with a model obeying standard geometry within 0.011 A in bond lengths and 1.91 degrees in bond angles. The BphC enzyme is a homo-octamer and each subunit is composed of two domains: Domain 1 (N-terminal part) and Domain 2 (C-terminal part). Each domain contains two repetitions of a novel folding motif (the "beta alpha beta beta beta" motif) each consisting of ca 55 amino acid residues. A single Fe ion in the active site coordinates the side-chains of three amino acid residues (His145, His209 and Glu260) and two solvent molecules. The coordination geometry is that of a square pyramid. In addition to the free form of the BphC enzyme, we have solved two three-dimensional structures of the BphC enzyme complexed with its substrates, 2,3-dihydroxybiphenyl (2,3-DHBP) or 3-methylcatechol (3-MCT). These substrates were found intact in the active site probably because of the oxidation of the Fe ion into ferric form (as judged by EPR spectra) in the present crystals. In both of the two substrate complexes, the two hydroxyl groups of the substrate, together with the three enzymatic side-chain ligands, were found to form a penta-coordinated system around the Fe ion roughly arranged in a trigonal bipyramidal configuration. The active site structures appear to be essentially consistent with the reaction mechanism proposed so far.
 
  Selected figure(s)  
 
Figure 10.
Figure 10. Proposed reaction mechanism common for the BphC enzyme and the related extradiol type dioxygenases. This is a modifi- cation of the previously proposed ones (Howard & Rees, 1991; Harayama et al., 1992). C1 and C2 positions on the catechol ring are indicated in (b).
Figure 11.
Figure 11. Least-squares fitting of the active site of the 3,4-PCD enzyme (hatched line; Ohrendorf et al., 1994) with that of the BphC-2,3-DHBP complex (solid line; present study). The following pairs of atoms (BphC atoms followed by 3,4-PCD atoms) were used for the least-squares fitting: (O3(2,3-DHBP)-O h (Tyr447)), (N e (His209)-N e (His462)), (N e (His145)-N e (His460)), (O e (Glu260)-O h (Tyr408)) and (O2(2,3-DHBP)-Water), where O2 and O3 are the oxygen atoms attached to C2 and C3 atoms of 2,3-DHBP respectively (see Figure 1). The least-squares fitting was carried out with respect to the Fe ions and the above-mentioned pairs of corresponding atoms resulting in an r.m.s deviation of 0.39 Å .
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1996, 255, 735-752) copyright 1996.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18277980 E.G.Kovaleva, and J.D.Lipscomb (2008).
Versatility of biological non-heme Fe(II) centers in oxygen activation reactions.
  Nat Chem Biol, 4, 186-193.  
19007887 J.D.Lipscomb (2008).
Mechanism of extradiol aromatic ring-cleaving dioxygenases.
  Curr Opin Struct Biol, 18, 644-649.  
18558332 K.Furukawa, and H.Fujihara (2008).
Microbial degradation of polychlorinated biphenyls: biochemical and molecular features.
  J Biosci Bioeng, 105, 433-449.  
17446402 E.G.Kovaleva, and J.D.Lipscomb (2007).
Crystal structures of Fe2+ dioxygenase superoxo, alkylperoxo, and bound product intermediates.
  Science, 316, 453-457.
PDB codes: 2ig9 2iga
17567087 E.G.Kovaleva, M.B.Neibergall, S.Chakrabarty, and J.D.Lipscomb (2007).
Finding intermediates in the O2 activation pathways of non-heme iron oxygenases.
  Acc Chem Res, 40, 475-483.  
17526781 Y.Morono, W.Kitagawa, N.Kimura, N.Noda, K.Nakamura, and Y.Kamagata (2007).
"Mark the gene": a method for nondestructive introduction of marker sequences inside the gene frame of transgenes.
  Appl Environ Microbiol, 73, 4915-4921.  
16477023 H.Sugimoto, S.Oda, T.Otsuki, T.Hino, T.Yoshida, and Y.Shiro (2006).
Crystal structure of human indoleamine 2,3-dioxygenase: catalytic mechanism of O2 incorporation by a heme-containing dioxygenase.
  Proc Natl Acad Sci U S A, 103, 2611-2616.
PDB codes: 2d0t 2d0u
16217642 J.P.Emerson, M.L.Wagner, M.F.Reynolds, L.Que, M.J.Sadowsky, and L.P.Wackett (2005).
The role of histidine 200 in MndD, the Mn(II)-dependent 3,4-dihydroxyphenylacetate 2,3-dioxygenase from Arthrobacter globiformis CM-2, a site-directed mutagenesis study.
  J Biol Inorg Chem, 10, 751-760.  
15715866 J.Wesche, E.Hammer, D.Becher, G.Burchhardt, and F.Schauer (2005).
The bphC gene-encoded 2,3-dihydroxybiphenyl-1,2-dioxygenase is involved in complete degradation of dibenzofuran by the biphenyl-degrading bacterium Ralstonia sp. SBUG 290.
  J Appl Microbiol, 98, 635-645.  
15739104 K.D.Koehntop, J.P.Emerson, and L.Que (2005).
The 2-His-1-carboxylate facial triad: a versatile platform for dioxygen activation by mononuclear non-heme iron(II) enzymes.
  J Biol Inorg Chem, 10, 87-93.  
15659662 R.Endo, M.Kamakura, K.Miyauchi, M.Fukuda, Y.Ohtsubo, M.Tsuda, and Y.Nagata (2005).
Identification and characterization of genes involved in the downstream degradation pathway of gamma-hexachlorocyclohexane in Sphingomonas paucimobilis UT26.
  J Bacteriol, 187, 847-853.  
15487948 C.K.Brown, M.W.Vetting, C.A.Earhart, and D.H.Ohlendorf (2004).
Biophysical analyses of designed and selected mutants of protocatechuate 3,4-dioxygenase1.
  Annu Rev Microbiol, 58, 555-585.
PDB codes: 2bum 2buq 2bur 2but 2buv
15583384 K.Iwata, H.Noguchi, Y.Usami, J.W.Nam, Z.Fujimoto, H.Mizuno, H.Habe, H.Yamane, T.Omori, and H.Nojiri (2004).
Crystallization and preliminary crystallographic analysis of the 2'-aminobiphenyl-2,3-diol 1,2-dioxygenase from the carbazole-degrader Pseudomonas resinovorans strain CA10.
  Acta Crystallogr D Biol Crystallogr, 60, 2340-2342.  
12728990 K.Iwata, H.Nojiri, K.Shimizu, T.Yoshida, H.Habe, and T.Omori (2003).
Expression, purification, and characterization of 2'-aminobiphenyl-2,3-diol 1,2-dioxygenase from carbazole-degrader Pseudomonas resinovorans strain CA10.
  Biosci Biotechnol Biochem, 67, 300-307.  
14529267 P.Liu, A.Liu, F.Yan, M.D.Wolfe, J.D.Lipscomb, and H.W.Liu (2003).
Biochemical and spectroscopic studies on (S)-2-hydroxypropylphosphonic acid epoxidase: a novel mononuclear non-heme iron enzyme.
  Biochemistry, 42, 11577-11586.  
12672826 T.Hatta, G.Mukerjee-Dhar, J.Damborsky, H.Kiyohara, and K.Kimbara (2003).
Characterization of a novel thermostable Mn(II)-dependent 2,3-dihydroxybiphenyl 1,2-dioxygenase from a polychlorinated biphenyl- and naphthalene-degrading Bacillus sp. JF8.
  J Biol Chem, 278, 21483-21492.  
12047377 L.Hörnsten, C.Su, A.E.Osbourn, U.Hellman, and E.H.Oliw (2002).
Cloning of the manganese lipoxygenase gene reveals homology with the lipoxygenase gene family.
  Eur J Biochem, 269, 2690-2697.  
12224629 T.Iida, Y.Mukouzaka, K.Nakamura, I.Yamaguchi, and T.Kudo (2002).
Isolation and characterization of dibenzofuran-degrading actinomycetes: analysis of multiple extradiol dioxygenase genes in dibenzofuran-degrading Rhodococcus species.
  Biosci Biotechnol Biochem, 66, 1462-1472.  
12121648 T.W.Martin, Z.Dauter, Y.Devedjiev, P.Sheffield, F.Jelen, M.He, D.H.Sherman, J.Otlewski, Z.S.Derewenda, and U.Derewenda (2002).
Molecular basis of mitomycin C resistance in streptomyces: structure and function of the MRD protein.
  Structure, 10, 933-942.
PDB codes: 1kll 1kmz
11470438 A.A.McCarthy, H.M.Baker, S.C.Shewry, M.L.Patchett, and E.N.Baker (2001).
Crystal structure of methylmalonyl-coenzyme A epimerase from P. shermanii: a novel enzymatic function on an ancient metal binding scaffold.
  Structure, 9, 637-646.
PDB codes: 1jc4 1jc5
11244073 U.Riegert, S.Bürger, and A.Stolz (2001).
Altering catalytic properties of 3-chlorocatechol-oxidizing extradiol dioxygenase from Sphingomonas xenophaga BN6 by random mutagenesis.
  J Bacteriol, 183, 2322-2330.  
10633115 E.Andújar, M.J.Hernáez, S.R.Kaschabek, W.Reineke, and E.Santero (2000).
Identification of an extradiol dioxygenase involved in tetralin biodegradation: gene sequence analysis and purification and characterization of the gene product.
  J Bacteriol, 182, 789-795.  
12483570 K.Furukawa (2000).
Biochemical and genetic bases of microbial degradation of polychlorinated biphenyls (PCBs).
  J Gen Appl Microbiol, 46, 283-296.  
10891075 M.W.Vetting, D.A.D'Argenio, L.N.Ornston, and D.H.Ohlendorf (2000).
Structure of Acinetobacter strain ADP1 protocatechuate 3, 4-dioxygenase at 2.2 A resolution: implications for the mechanism of an intradiol dioxygenase.
  Biochemistry, 39, 7943-7955.
PDB codes: 1eo2 1eo9 1eoa 1eob 1eoc
10801478 M.W.Vetting, and D.H.Ohlendorf (2000).
The 1.8 A crystal structure of catechol 1,2-dioxygenase reveals a novel hydrophobic helical zipper as a subunit linker.
  Structure, 8, 429-440.
PDB codes: 1dlm 1dlq 1dlt 1dmh
  9973359 A.E.Mars, J.Kingma, S.R.Kaschabek, W.Reineke, and D.B.Janssen (1999).
Conversion of 3-chlorocatechol by various catechol 2,3-dioxygenases and sequence analysis of the chlorocatechol dioxygenase region of Pseudomonas putida GJ31.
  J Bacteriol, 181, 1309-1318.  
10368270 A.Kita, S.Kita, I.Fujisawa, K.Inaka, T.Ishida, K.Horiike, M.Nozaki, and K.Miki (1999).
An archetypical extradiol-cleaving catecholic dioxygenase: the crystal structure of catechol 2,3-dioxygenase (metapyrocatechase) from Ppseudomonas putida mt-2.
  Structure, 7, 25-34.
PDB code: 1mpy
10393920 A.M.Rocklin, D.L.Tierney, V.Kofman, N.M.Brunhuber, B.M.Hoffman, R.E.Christoffersen, N.O.Reich, J.D.Lipscomb, and L.Que (1999).
Role of the nonheme Fe(II) center in the biosynthesis of the plant hormone ethylene.
  Proc Natl Acad Sci U S A, 96, 7905-7909.  
  9922262 B.E.Haigler, G.R.Johnson, W.C.Suen, and J.C.Spain (1999).
Biochemical and genetic evidence for meta-ring cleavage of 2,4, 5-trihydroxytoluene in Burkholderia sp. strain DNT.
  J Bacteriol, 181, 965-972.  
10607676 C.J.Schofield, and Z.Zhang (1999).
Structural and mechanistic studies on 2-oxoglutarate-dependent oxygenases and related enzymes.
  Curr Opin Struct Biol, 9, 722-731.  
10600135 E.L.Hegg, A.K.Whiting, R.E.Saari, J.McCracken, R.P.Hausinger, and L.Que (1999).
Herbicide-degrading alpha-keto acid-dependent enzyme TfdA: metal coordination environment and mechanistic insights.
  Biochemistry, 38, 16714-16726.  
  10518716 F.Brühlmann, and W.Chen (1999).
Transformation of polychlorinated biphenyls by a novel BphA variant through the meta-cleavage pathway.
  FEMS Microbiol Lett, 179, 203-208.  
  10542173 K.Miyauchi, Y.Adachi, Y.Nagata, and M.Takagi (1999).
Cloning and sequencing of a novel meta-cleavage dioxygenase gene whose product is involved in degradation of gamma-hexachlorocyclohexane in Sphingomonas paucimobilis.
  J Bacteriol, 181, 6712-6719.  
10467151 K.Sugimoto, T.Senda, H.Aoshima, E.Masai, M.Fukuda, and Y.Mitsui (1999).
Crystal structure of an aromatic ring opening dioxygenase LigAB, a protocatechuate 4,5-dioxygenase, under aerobic conditions.
  Structure, 7, 953-965.
PDB codes: 1b4u 1bou
10467142 L.Serre, A.Sailland, D.Sy, P.Boudec, A.Rolland, E.Pebay-Peyroula, and C.Cohen-Addad (1999).
Crystal structure of Pseudomonas fluorescens 4-hydroxyphenylpyruvate dioxygenase: an enzyme involved in the tyrosine degradation pathway.
  Structure, 7, 977-988.
PDB code: 1cjx
  10427057 M.Seeger, M.Zielinski, K.N.Timmis, and B.Hofer (1999).
Regiospecificity of dioxygenation of di- to pentachlorobiphenyls and their degradation to chlorobenzoates by the bph-encoded catabolic pathway of Burkholderia sp. strain LB400.
  Appl Environ Microbiol, 65, 3614-3621.  
  10438749 U.Riegert, G.Heiss, A.E.Kuhm, C.Müller, M.Contzen, H.J.Knackmuss, and A.Stolz (1999).
Catalytic properties of the 3-chlorocatechol-oxidizing 2, 3-dihydroxybiphenyl 1,2-dioxygenase from Sphingomonas sp. strain BN6.
  J Bacteriol, 181, 4812-4817.  
9671502 A.P.Saint-Jean, K.R.Phillips, D.J.Creighton, and M.J.Stone (1998).
Active monomeric and dimeric forms of Pseudomonas putida glyoxalase I: evidence for 3D domain swapping.
  Biochemistry, 37, 10345-10353.  
9634695 B.Kauppi, K.Lee, E.Carredano, R.E.Parales, D.T.Gibson, H.Eklund, and S.Ramaswamy (1998).
Structure of an aromatic-ring-hydroxylating dioxygenase-naphthalene 1,2-dioxygenase.
  Structure, 6, 571-586.
PDB code: 1ndo
9857017 F.H.Vaillancourt, S.Han, P.D.Fortin, J.T.Bolin, and L.D.Eltis (1998).
Molecular basis for the stabilization and inhibition of 2, 3-dihydroxybiphenyl 1,2-dioxygenase by t-butanol.
  J Biol Chem, 273, 34887-34895.
PDB codes: 1kmy 1knd 1knf
9818186 J.A.Gerlt, and P.C.Babbitt (1998).
Mechanistically diverse enzyme superfamilies: the importance of chemistry in the evolution of catalysis.
  Curr Opin Chem Biol, 2, 607-612.  
  10082363 M.Bergdoll, L.D.Eltis, A.D.Cameron, P.Dumas, and J.T.Bolin (1998).
All in the family: structural and evolutionary relationships among three modular proteins with diverse functions and variable assembly.
  Protein Sci, 7, 1661-1670.  
9761924 M.Q.Chen, C.C.Yin, W.Zhang, Y.M.Mao, and Z.H.Zhang (1998).
Purification, crystallization and preliminary X-ray diffraction studies on the thermostable catechol 2,3-dioxygenase of Bacillus stearothermophilus expressed in Escherichia coli.
  Acta Crystallogr D Biol Crystallogr, 54, 446-447.  
9667935 S.J.Lange, and L.Que (1998).
Oxygen activating nonheme iron enzymes.
  Curr Opin Chem Biol, 2, 159-172.  
  9603871 U.Riegert, G.Heiss, P.Fischer, and A.Stolz (1998).
Distal cleavage of 3-chlorocatechol by an extradiol dioxygenase to 3-chloro-2-hydroxymuconic semialdehyde.
  J Bacteriol, 180, 2849-2853.  
  9647824 X.Peng, T.Egashira, K.Hanashiro, E.Masai, S.Nishikawa, Y.Katayama, K.Kimbara, and M.Fukuda (1998).
Cloning of a Sphingomonas paucimobilis SYK-6 gene encoding a novel oxygenase that cleaves lignin-related biphenyl and characterization of the enzyme.
  Appl Environ Microbiol, 64, 2520-2527.  
9218781 A.D.Cameron, B.Olin, M.Ridderström, B.Mannervik, and T.A.Jones (1997).
Crystal structure of human glyoxalase I--evidence for gene duplication and 3D domain swapping.
  EMBO J, 16, 3386-3395.
PDB code: 1fro
9254600 A.M.Orville, J.D.Lipscomb, and D.H.Ohlendorf (1997).
Crystal structures of substrate and substrate analog complexes of protocatechuate 3,4-dioxygenase: endogenous Fe3+ ligand displacement in response to substrate binding.
  Biochemistry, 36, 10052-10066.
PDB codes: 3pca 3pcj 3pck 3pcl 3pcm
  8981980 A.Schmid, B.Rothe, J.Altenbuchner, W.Ludwig, and K.H.Engesser (1997).
Characterization of three distinct extradiol dioxygenases involved in mineralization of dibenzofuran by Terrabacter sp. strain DPO360.
  J Bacteriol, 179, 53-62.  
9434907 C.J.Schofield, J.E.Baldwin, M.F.Byford, I.Clifton, J.Hajdu, C.Hensgens, and P.Roach (1997).
Proteins of the penicillin biosynthesis pathway.
  Curr Opin Struct Biol, 7, 857-864.  
9461283 E.L.Hegg, and L.Que (1997).
The 2-His-1-carboxylate facial triad--an emerging structural motif in mononuclear non-heme iron(II) enzymes.
  Eur J Biochem, 250, 625-629.  
9406548 H.Erlandsen, F.Fusetti, A.Martinez, E.Hough, T.Flatmark, and R.C.Stevens (1997).
Crystal structure of the catalytic domain of human phenylalanine hydroxylase reveals the structural basis for phenylketonuria.
  Nat Struct Biol, 4, 995.
PDB code: 1pah
9228951 K.E.Goodwill, C.Sabatier, C.Marks, R.Raag, P.F.Fitzpatrick, and R.C.Stevens (1997).
Crystal structure of tyrosine hydroxylase at 2.3 A and its implications for inherited neurodegenerative diseases.
  Nat Struct Biol, 4, 578-585.
PDB code: 1toh
  9244273 S.I.Sato, N.Ouchiyama, T.Kimura, H.Nojiri, H.Yamane, and T.Omori (1997).
Cloning of genes involved in carbazole degradation of Pseudomonas sp. strain CA10: nucleotide sequences of genes and characterization of meta-cleavage enzymes and hydrolase.
  J Bacteriol, 179, 4841-4849.  
9047314 Y.R.Boldt, A.K.Whiting, M.L.Wagner, M.J.Sadowsky, L.Que, and L.P.Wackett (1997).
Manganese(II) active site mutants of 3,4-dihydroxyphenylacetate 2,3-dioxygenase from Arthrobacter globiformis strain CM-2.
  Biochemistry, 36, 2147-2153.  
  8655491 H.Jiang, R.E.Parales, N.A.Lynch, and D.T.Gibson (1996).
Site-directed mutagenesis of conserved amino acids in the alpha subunit of toluene dioxygenase: potential mononuclear non-heme iron coordination sites.
  J Bacteriol, 178, 3133-3139.  
  8830689 L.D.Eltis, and J.T.Bolin (1996).
Evolutionary relationships among extradiol dioxygenases.
  J Bacteriol, 178, 5930-5937.  
  8702262 M.Sylvestre, Y.Hurtubise, D.Barriault, J.Bergeron, and D.Ahmad (1996).
Characterization of active recombinant 2,3-dihydro-2,3-dihydroxybiphenyl dehydrogenase from Comamonas testosteroni B-356 and sequence of the encoding gene (bphB).
  Appl Environ Microbiol, 62, 2710-2715.  
9022704 P.L.Roach, I.J.Clifton, C.M.Hensgens, N.Shibata, A.J.Long, R.W.Strange, S.S.Hasnain, C.J.Schofield, J.E.Baldwin, and J.Hajdu (1996).
Anaerobic crystallisation of an isopenicillin N synthase.Fe(II).substrate complex demonstrated by X-ray studies.
  Eur J Biochem, 242, 736-740.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.